refactor: update standalone scripts

Author: Yunuuuu

DESCRIPTION

@@ -23,7 +23,7 @@ Imports:
     MCMCpack,
     methods,
     openEBGM,
-    rlang (>= 1.1.0),
+    rlang,
     rvest,
     tools,
     utils,
@@ -58,6 +58,7 @@ Collate:
     'import-standalone-assert.R'
     'import-standalone-cli.R'
     'import-standalone-obj-type.R'
+    'import-standalone-pkg.R'
     'load.R'
     'merge.R'
     'meta.R'
@@ -71,6 +72,7 @@ Collate:
     'signal.R'
     'standardize.R'
     'unify.R'
+    'utils-assert.R'
     'utils-file.R'
     'utils-str.R'
     'utils.R'

NAMESPACE

@@ -75,6 +75,7 @@ exportMethods(meddra_version)
 exportMethods(show)
 importClassesFrom(data.table,data.table)
 importFrom(BiocParallel,SerialParam)
+importFrom(cli,qty)
 importFrom(data.table,"%chin%")
 importFrom(data.table,":=")
 importFrom(data.table,.BY)
@@ -86,3 +87,11 @@ importFrom(data.table,.NGRP)
 importFrom(data.table,.SD)
 importFrom(data.table,data.table)
 importFrom(methods,show)
+importFrom(rlang,abort)
+importFrom(rlang,caller_arg)
+importFrom(rlang,caller_env)
+importFrom(rlang,ffi_standalone_check_number_1.0.7)
+importFrom(rlang,ffi_standalone_is_bool_1.0.7)
+importFrom(rlang,is_missing)
+importFrom(rlang,is_string)
+importFrom(rlang,is_vector)

R/athena.R

@@ -15,7 +15,7 @@
 athena <- function(use = NULL, list = FALSE, force = FALSE, url = NULL) {
     assert_bool(list)
     assert_bool(force)
-    assert_string(url, null_ok = TRUE)
+    assert_string(url, allow_null = TRUE)
     if (!is.null(url) && !startsWith(url, "https")) {
         cli::cli_abort("{.arg url} must start with {.val https}")
     }
@@ -24,7 +24,7 @@ athena <- function(use = NULL, list = FALSE, force = FALSE, url = NULL) {
     if (list) {
         list.files(path)
     } else {
-        assert_inclusive(use, use_athena, null_ok = TRUE)
+        assert_inclusive(use, use_athena, allow_null = TRUE)
         use <- use %||% use_athena
         out <- athena_loads(path, use)
         if (length(use) == 1L) {

R/available.R

@@ -13,7 +13,7 @@
 #' faers_available(c(2011, 2023), c("q1", "q2"))
 #' @export
 faers_available <- function(years, quarters, force = FALSE, internal = FALSE) {
-    assert_inclusive(quarters, faers_file_quarters)
+    assert_inclusive(quarters, FAERS_FILE_QUARTERS)
     metadata <- faers_meta(force = force, internal = internal)
     years %in% metadata$year & quarters %chin% metadata$quarter
 }

R/class-FAERS.R

@@ -71,10 +71,10 @@ validate_faers <- function(object) {
     if (length(object@year) != length(object@quarter)) {
         return("the length of `@year` and `@quarter` must be the same")
     }
-    if (!all(object@quarter %chin% faers_file_quarters)) {
+    if (!all(object@quarter %chin% FAERS_FILE_QUARTERS)) {
         return(sprintf(
             "`@quarter` must be values in %s",
-            oxford_comma(faers_file_quarters, final = "or")
+            oxford_comma(FAERS_FILE_QUARTERS, final = "or")
         ))
     }
     if (anyDuplicated(faers_period(object))) {
@@ -87,10 +87,10 @@ validate_faers <- function(object) {
     if (length(object@deduplication) != 1L || is.na(object@deduplication)) {
         return("@deduplication must be a bool, `TRUE` or `FALSE`")
     }
-    if (!rlang::is_string(object@format, faers_file_format)) {
+    if (!rlang::is_string(object@format, FAERS_FILE_FORMAT)) {
         return(sprintf(
             "`@format` must be a string of %s",
-            oxford_comma(faers_file_format, final = "or")
+            oxford_comma(FAERS_FILE_FORMAT, final = "or")
         ))
     }
     TRUE
@@ -114,9 +114,9 @@ methods::setClass(
 
 methods::setValidity("FAERSascii", function(object) {
     data <- object@data
-    if (!all(faers_ascii_file_fields %chin% names(data))) {
+    if (!all(FAERS_ASCII_FILE_FIELDS %chin% names(data))) {
         return(sprintf(
-            "`@data` must contain the all ascii fields, including %s", oxford_comma(faers_ascii_file_fields)
+            "`@data` must contain the all ascii fields, including %s", oxford_comma(FAERS_ASCII_FILE_FIELDS)
         ))
     }
     if (!all(vapply(data, data.table::is.data.table, logical(1L)))) {

R/combine.R

@@ -135,13 +135,13 @@ combine_faers_data <- function(x, type) {
 }
 
 combine_faers_ascii_data <- function(x) {
-    data_list <- lapply(faers_ascii_file_fields, function(field) {
+    data_list <- lapply(FAERS_ASCII_FILE_FIELDS, function(field) {
         data.table::rbindlist(
             lapply(x, function(obj) obj@data[[field]]),
             fill = TRUE, use.names = TRUE
         )
     })
-    data.table::setattr(data_list, "names", faers_ascii_file_fields)
+    data.table::setattr(data_list, "names", FAERS_ASCII_FILE_FIELDS)
     data_list
 }
 

R/download.R

@@ -19,8 +19,8 @@
 #' )
 #' @export
 faers_download <- function(years, quarters, format = NULL, dir = getwd(), ...) {
-    format <- match.arg(format, faers_file_format)
-    assert_string(dir, empty_ok = FALSE)
+    format <- match.arg(format, FAERS_FILE_FORMAT)
+    assert_string(dir, allow_empty = FALSE)
     if (format == "xml") {
         # only faers database has xml data files
         is_aers_pairs <- is_from_laers(years, quarters)

R/faers.R

@@ -12,7 +12,7 @@
 #' )
 #' @export
 faers <- function(years, quarters, format = NULL, dir = getwd(), compress_dir = dir, handle_opts = list()) {
-    format <- match.arg(format, faers_file_format)
+    format <- match.arg(format, FAERS_FILE_FORMAT)
     yq <- recycle_scalar(years = years, quarters = quarters)
     data.table::setDT(yq)
     yq <- unique(yq)

R/fda_drugs.R

@@ -20,7 +20,7 @@ fda_drugs <- function(pattern = "Products", url = NULL,
                       list = FALSE, force = FALSE) {
     assert_bool(list)
     assert_bool(force)
-    assert_string(url, null_ok = TRUE)
+    assert_string(url, allow_null = TRUE)
     file <- fda_drugs_file(url, force)
     fda_drugs_load(file, pattern = pattern, list = list)
 }